<div dir="ltr">I'm a bit confused about what is going on with my autobuild run. 狢 solved a structure from anomalous data to 2.7A but many loops are missing. 狢 ran phaser with the current model and native data that extends to 2.4A and got a solution and started autobuild from there. 狢 used mostly the default settings and rebuild_in_place=False. 鼦fter a pretty short time I realized the run was over and at the bottom of the log I see this:<div>
<br></div><div><p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Cycle 3� R/Rfree=0.28/0.35� Built=488� Placed=467</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">AutoBuild_build_cycle� AutoBuild� Run 162 Fri Sep� 6 14:33:39 2013</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Deciding if we should continue...</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Recent R change per cycle:� 0.0</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Ending these build cycles as the recent change in R per cycle has been�</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">0.0 and the required value of change� is� -0.005</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">and the R is somewhat acceptable at 0.276670644792</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">All done with build cycles in this region</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">AutoBuild_set_up_build� AutoBuild� Run 162 Fri Sep� 6 14:33:40 2013</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">All omit/non-omit regions completed</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">finished� AutoBuild� Run 162 Fri Sep� 6 14:33:40 2013</p>
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Finishing� AutoBuild Run 162</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Facts written to AutoBuild_run_162_/AutoBuild_Facts.dat</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">AutoBuild Run 162</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Summary of model-building for run 162� Fri Sep� 6 14:33:40 2013</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Files are in the directory:� /Users/heather/Desktop/M/AutoBuild_run_162_/</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Starting mtz file: /Users/heather/Desktop/M/ImportRawData_run_4_/A-3_xx_PHX.mtz</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Sequence file: /Users/heather/Desktop/M/m.pir</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Best solution on cycle: 2� � R/Rfree=0.26/0.33</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">Summary of output files for Solution 1 from rebuild cycle 2</p>
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<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">---� Model (PDB file)� ---</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">---� Model (CIF file)� ---</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">cif_pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.cif</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">---� Refinement log file ---</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">log_refine: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_refine</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">---� Model-building log file ---</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">log: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">---� Model-map correlation log file ---</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">log_eval: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_eval</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">---� 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PHFOFCWT ---</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">refine_map_coeffs: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_map_coeffs.mtz</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">---� Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag ---</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">refine_data: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">---� Density-modified map coefficients FWT PHWT ---</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">denmod_map_coeffs: /Users/heather/Desktop//AutoBuild_run_162_/overall_best_denmod_map_coeffs.mtz</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">You might consider making one very good model now with:�</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">phenix.autobuild \</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">賷ata=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz \</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">𦅙odel=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb \</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">�rebuild_in_place=True \</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier">坟eq_file=/Users/heather/Desktop/M/m.pir</p>
<p style="margin:0.0px 0.0px 0.0px 0.0px;font:11.0px Courier;min-height:13.0px"><br></p><div>My full sequence is 325 amino acids so only about 75% is build in. 狢 am hoping autobuild can help find at least some of these missing residues. �Why would the change in R be zero? What is meant by "You might consider making one very good model now with:"? 狢 tried running autobuild with these new files and rebuild_in_place=true and get the same type of message. 狢s this the best that autobuild蠏an do? 狢 also ran the phaser solution through refinement and can significantly lower the Rs from 0.26/0.33 to 0.22/0.30. 狢 appreciate any advice on how best to proceed. �</div>
</div><div><br></div><div>I am using 1.8.2-1472 if that matters.</div><div><br></div><div><br></div><div>Thanks,</div><div>Heather</div></div>